3 papers
cs.LG2026
Structure-Aware Masking for Protein Representation Learning
Thomas Walton, Ayan Goel, Amirali Aghazadeh
Masked language modeling (MLM) is the standard objective for training protein language models, typically implemented by randomly masking individual residues at a fixed rate (e.g.,…
cs.CL2026
Link Prediction for Event Logs in the Process Industry
Anastasia Zhukova, Thomas Walton, Christian E. Lobmüller +1
In the era of graph-based retrieval-augmented generation (RAG), link prediction is a significant preprocessing step for improving the quality of fragmented or incomplete domain-spe…
cs.LG2025
SpecMER: Fast Protein Generation with K-mer Guided Speculative Decoding
Thomas Walton, Darin Tsui, Aryan Musharaf +1
Autoregressive models have transformed protein engineering by enabling the generation of novel protein sequences beyond those found in nature. However, their sequential inference i…